The Emperor Protects
by MrDarth151
Summary: When the Imperium is thrown into unfamiliar universe, changes are inevitable. Will they be for better or worse, it remains to be seen. But, one thing is certain. One day, there will be war. And it is the craft mankind knows best. Cover created by GENZOMAN from Deviantart.
1. Prologue

Disclaimer: I do not own Warhammer 40000, Mass Effect, or any work based in those two universes. They are property of their respective owners, namely Games Workshop, Electronis Arts, Black Library, Bioware, Relic, THQ and/or their respective authors.

* * *

**It is the third millennium. The Emperor, clad in His golden armor, leads the humanity out of the darkness. By His own will and power, He is the master of mankind and the lord of thousands worlds. He is the protector and the greatest champion of humanity in history.**

**His armies are vast and powerful. Countless soldiers of planetary defence forces, supported by the thousands Imperial Guard regiments, and the might of the Imperial Fleet, are constantly guarding the worlds of the Imperium. Great fleets of the Adeptus Mechanicus travel throughout the galaxy, searching for the technology long lost, in their endless Quest for Knowledge. Imperium greatest warriors, eighteen legions of Adeptus Astartes, lead by Primarchs, create and raised on Terra by the Emperor, are vigilant, and always ready to destroy anything that threatens mankind. **

**And yet, there is no war. And the laughter of thirsting gods is not heard. For it is the time of mysteries. Worlds are found, stripped from live, but not from architecture and cities. Only traitorous humans threaten the peace in the Imperium. The mysterious alien relics are examined by tech-priests. And as the Inquisition searches for answers, mankind takes last, desperate breath. It is calm before the storm. The moment of serenity, right before plunging into abyss of terror. **

**These are the tales of those times.**

* * *

Author notes: Well, that is short. But in those 223 words you will find basic fundations of my entire story. I also wanted to have Black Library style prologue. Just because I can.

I want to thank Ursakar, author of the best ME/WH40k crossover yet, The Mission Stays the Same. It is a great inspiration for me, even if I disagree on some points with his interpretations of the WH40k characters. You have set the bar high, my good sir, but i hope to create story a least half as well written as yours.

With that out of the way, lets get to the premise of this work of fiction. This is WH40k/ME crossover. It will feature entire Imperium in the ME universe, and will go on from there. Mind you, this is a pre-heresy Imperium, so do not, I repeat, do not expect the religious side of the Imperium to be present in this story. Also, I'm aware of all the exceptions I took from WH40k canon. They are deliberate, and are tied to the rest of the story. I may be a aspiring writer, but I know my source material.

I do not have beta at the moment, so all mistakes I made are mine, and I would be pleased if you point them out to me. Especially grammatical errors, since it is my first story written entirely in english, and I am always willing to improve.


	2. Chapter One: Arrivals

Disclaimer: I do not own Warhammer 40000, Mass Effect, or any work based in those two universes except for my own. They are property of their respective owners, namely Games Workshop, Electronis Arts, Black Library, Bioware, Relic, and/or their respective authors. Also, I'm aware of all the exceptions I took from WH40k canon. They are deliberate, and are tied to the rest of the story.

* * *

Chapter One: Arrivals.

2756167.M3.

Conquest Class Star Galleon 'Honored Pirate'

Orbit of planet Alpha

Corporal Jonathan Parlan was, frankly, terrified. His hands were shaking, while he stood before the doors to „Honored Pirate" guest quarters. Reputation of a man currently living there did not improve his chances in any way. Jonathan knew enough to be afraid. The very first thing that man did after boarding spoke values about him. He executed the First Officer, who dared to question the purpose of changing course to relatively unknown world, and then threatened the Captain.

„Any further signs of uncooperation will result in revoking your Warrant of Trade." Were his exact words. The very idea of someone having the power to revoke the Warrant was unthinkable. The captains Warrant was sign by Lord Horus himself. And there were very few persons in the universe that held more power than Lord Horus.

And then, there were whispers. In closed spaces of the ship, among the sixty five thousands crew members, rumors were bound to spread. But even so, this time they seemed... deliberate. Like the story of five ranking officers, who decided to avenge Firsts dead, only to mysteriously disappear. Or the mysterious noises coming from the guest quarters. Or even accusations of performing magic...

Walking on such rituals meant certain death. He would have been killed for even witnessing them. Or worse... use as a part of them.

Yet Parlan straighten himself, and steadied his breath. He was the Captains messenger. And he was given an order. His failure to accomplish such a simple task would certainly lead to being court marshaled. Or summary execution, depending on Captains mood. Taking deep breath and thinking that it was probably his last, he knocked on the door.

As muffled „Enter!" was heard, Corporal Jonathan Parlan did exactly as he was told.

What he saw surprised him greatly. Eviscerated corpses were nowhere to be seen, no demons were being summoned. Instead, the room was turned into an office, evidently with efficiency in mind. The resident of said room was sitting on rather comfortable looking couch, reading through some files. In the background, a servo-skull was searching through some files. It all looked like working place of some Ordinate of Adeptus Administratum.

Except for one thing. In the corner of the room, there was an armor. It was the most magnificent, state of the art, power armor Parlan ever saw. White and gold in colors, it bear two marks that were making it even more impressive. The first one was double headed eagle on the chest plate. The Imperial Aquila. The right to bear it was the sign of recognition, a privilege given personally by The Emperor. The other was the symbol on armors left pauldron. The symbol that almost everyone in the Imperium feared.

The sigil of the Imperial Inquisition.

„Yes?" The current owner of the room asked in rather pleasant, albeit cold tone. It was his eyes that unnerved the Jonathan the most, though. Scarlet red irises, with a unique pattern to them. It felt like he was being read, thoroughly. A felling he certainly didn't like.

Parlan cleared his throat, a little intimidated by the very presence of this man.

„My lord. There seems to be a slight problem with our shuttle. I'm afraid that your departure is going to be delayed." He could actually feel the slight shift in the atmosphere, when Lord Inquisitor focused his entire attention on him.

„I trust the matter is being dealt with as we speak?" He asked, his tone a bit colder than before. Parlan swallowed nervously, before answering.

„Yes, my lord. Our tech-priest assures me that the shuttle will be operational in less than an hour." Lord Inquisitors attention shifted, again, to the files lying before him. Only after that, Parlan was finally able to compose himself.

„So why are you still wasting my time, mister Parlan? Or do you have some other matters that require my attention?" The guest asked, with slight irritation in his voice.

„No..." Jonathan stumbled a little „ Not at all, my lord."

„Good. So now, you will go and inform the Captain that I will not tolerate any further delays. Is that clear?" Sheer malevolence of his voice made young Corporal shiver in fear.

„Yes, my lord. I will get to it immediately." He answered quickly, only to be dismissed with a quick wave of hand. He caught the opportunity and left the room, closing the door behind as quickly as he could, without being disrespectful. He had run for more than half of mile before a truly disturbing thought appeared in his mind.

„He knew my name." he whispered, and his words echoed through the empty corridors. His peace shattered, he started mumbling under his nose.

"Why...? Why did he... He knew my name... He... knew... my name... Why...? Why, why, why, why...?" he slowly faded away, into the darkcorners of the 'Honored Pirate'

* * *

As soon as Parlan left the room, Lord Inquisitor started laughing.

"Ha! Did you see his face, Mortimer? It was worth it, learning the names of every single potential messenger just for that moment. Hilarious." only silence has answered him. He sighed deeply. "Right. And I'm talking to a servo-skull again."

Frankly speaking, Lord Inquisitor Jack Harper was bored. And it was all Malcadors fault. Jack started to reread his orders once again, trying to make some sense of it.

++ Order number 128534 ++

++ Classification level Magenta ++

++ Subject: recent development on the planet Alpha. (Formerly known as Shanxi) ++

Lord Inquisitor Harper.

Your newest assignment is a matter of great importance. As such, I will require that you work alone. Even your own retinue cannot be trusted with this. You can use the local forces as you see fit, but be careful. You shall not disclose any of your information to them, unless necessary. Those with too much knowledge will be purged afterwards. You have been warned.

After you arrive to the system, you shall investigate the death of Inquisitor Gorgias Mateolus.I have forwarded all of information currently known to me. Use it well.

For the time being, you are given authority equal to that of the Warmaster, and myself. You are the Voice, and the Hand of the Emperor. Do not fail him. Do not fail me, Jack.

Malcador the Sigilate

Regent of Terra

High Lord of the Inquisition

Personal sigil of Malcador lied beneath his signature, a sign of authenticity and his personal interest in the matter. And materials attached to the order were... disturbing, to say the least.

"Mortimer, replay records number 79853 through 79865" theoretically, he could use neural connection, instead of voice interface, but the silence was slowly driving him insane.

Serwo-skull flew in front of him, and then started to display the messages.

++ Property of the Inquisition. ++

++ Unauthorized use will warrant immediate death sentence. ++

++ Records of Interrogations of 'Childrens of Anarchy' terrorist group. ++

++ Done by Inquisitor Gorgias Mateolous. ++

++ Record of day 1 found. Playing. ++

A face that appeared, that of young looking bald man with a goatee, obviously belonged to, now dead, Inquisitor.

"We finally managed to grab one! Yesterday, Arbites raid finally yield results. Judge Tutela has taken the leader of cell we crushed alive. Brilliant job on his part, to be honest." he moved from his spot, recording device following close by, heavily indicating that it was, in fact, his own servo-skull.

"That's an opportunity I have been waiting for. And I shall seize it. We may finally be able to crush the 'Childrens of Anarchy'!" Suddenly, he came to a stop, before the massive door. He waved at the two nearest Judges, while barking an order.

"Open it." to which they comply almost immediately and the two of them approached the consoles placed on both sides of the doors. They've entered their codes and the doors started to open, slowly. As soon they were open wide enough, Gorgias entered. His recorder soon followed the suit.

"My, my. Inquisitor Matelous! It's a pleasure, seeing you again!"

somebody said, with a clear happiness in his voice. Servo-skull entered the apparent interrogation room, giving a clear view of the prisoner.

He was… Remarkably unremarkable. "Pause the recording, Mortimer." Said the Inquisitor to his servo-skull.

Jack was actually… surprised was probably the proper word, he guessed. Every single time he viewed the footage, it managed to catch him off guard.

The Prisoner freeze in the frames of recording was the plainest man he has ever seen. There was literally nothing significant about him. In fact, Harper found it hard to even focus his attention on him; he has found himself focusing more on the Judges guarding the prisoner, then the prisoner himself. It was quite a thing. And a perfect one for a terrorist. It was strange, and as such, something to notice. Because a man like that should not exist.

"Resume the recording, Mortimer"

Inquisitors shake his head, still calm.

"I'm afraid that the feeling isn't mutual... Iota"

The only thing that answered him was a stunned silence. And then... a laughter?

"Ha, ha! Good one, Inquisitor! I would have given you a clap, but unfortunately, my hands are tied." He wiggled a little in his restrains. Gorgias frowned deeply, evidently tired of the mans antics.

"This is an Inquisitorial interrogation. Treat it as such!" he barked towards him. And even though it was only a recording, Jack could feel the change in the prisoner.

"Tsk, tsk, tsk." The prisoner, or Iota, as he was apparently called, straightened himself. The restrains creaked, evidently barely holding him. Surprisingly, the guards maintained their stance, as if nothing was happening. It was his voice that broke their peace.

"And here I complemented you, Inquisitor." he responded, his tone of voice now low, cold, calculating. Threatening. Two Judges guarding the room instantly pointed their weapons at him. Iota seemed unbothered by two shotguns aiming at his head.

"Why, it would almost seem that you are not interested in proper, civilized conversation." he continued, his tone unchanged. Inquisitor seemed unchanged, although Jack could not see his face.

"I'm interested in truth. Not your childish behavior." His voiced also seemed unfazed. Jack had to give him credit; the man was not easily frightened. Iota didn't seem to care either way, since he responded in short, cold chuckle.

"The Truth, Inquisitor? Which truth could you possibly mean? My Truth? Yours? The Imperial Truth?" he spat out the last words. The amount of venom in those three words was truly impressive.

"I would prefer one that's most true of them"

"A wise decision. And the dangerous one. Can you handle the Truth... Inquisitor?"

As of now, Jack Harper didn't know the answer to that question. The recording suddenly cut, turning into static.

++ Record corrupted. Unable to proceed. ++

++ Record of day 2, erased. ++

++ Record of day 3, erased. ++

++ Record of day 4, erased. ++

++ Record of day 5, erased. ++

++ Record of day 6, erased. ++

++ Personal record number 1 found. Playing. ++

The Inquisitor that appeared on the recording looked a lot older, and more exhausted, than before. It was strange, like many things about this case. Harper knew rather well how much strain prolonged interrogation put on the interrogator, both mentally, and physically, but nothing to that degree.

"I'm getting close to the Truth." And yet, his voice was strong. Harper was apparently wrong about the reasons of exhaustion. Funny. He didn't noticed it the first time he watched the recording...

"I know it. Iota is surprisingly... cooperative. Although I'm no longer certain that it is a good thing." his voice sounded a little haunted there for a second. "No matter. I will find it. The Key in his words. It might change our future. Or it could be nothing. Both options are equally terrifying."

++ Record end. ++

++ Record of day 7, erased. ++

++ Record of day 8, erased. ++

++ Personal record number 2 found. Playing. ++

This time the fatigue on the Inquisitors face was even more apparent than before. And his gaze seemed a bit off, somehow. It was like... he was looking for something in shadows.

"I was right! The key is there. Iota is willing to tell me it, as unfortunate as that may be. And even though I'm no longer certain I want to, I must hear it. The very nature of it will change the Imperium. I'm sure of it."

++ Record end. ++

++ Record of day 9, erased. ++

++ Personal record number 3, erased. ++

++ No more records found. ++

Jack just sit there, for a moment, thinking. Something in those materials, made available to him by his superiors, drew attention of Malcador himself. The man never did anything without purpose, of that he was certain. And he could not figure out what it was. The only thing he could think of was the whole talk about the Key, but, he had to admit it, it sounded like the inane babble to him. Most likely, it was just exaggeration on Gorgias part. And even his murder, while certainly an important event, was not enough to give Jack the kind of power he was given. There were now three persons in the entire Imperium that eclipsed him in terms of political power: Malcador the Sigilate, Warmaster, and the Emperor himself. It was exciting, to say the least.

Such power would have driven lesser man insane. Harper was still in control, although his sanity was in question before.

And yet... Malcador saw something in there. What was it?

His train of thoughts was interrupted by a knock at the door. He sighed.

"Enter!" He shouted, slightly irritated. He could identify his guest as the new first officer. Funny, when he shot the last one, he did not think that a replacement will be so quick to appear.

"My Lord!" He said, with big smile on his face. "I'm happy to report that the shuttle is ready." His voice was filled with pride. Even though he probably had nothing to do with that development. Typical. Inquisitor nodded once, without thinking.

"Good, good... Well, I suppose you have brought man to carry my things, did you not?" He asked in rather neutral tones, there was no need to antagonize the man, after all. Also, killing the second first officer would have looked bad.

"Yes, my Lord!" Harper groaned a little. Another shout from this man would certainly earned him a bolter round to the brain. "They are ready, and have been instructed to not look at anything, as per your orders."

"Good. I would have hated to carry out more summary executions." Jack said, overseeing the whole ordeal. It seemed to him that everything was in order. He sighed again.

"Well, at least I will be able to look through the autopsy report and their personall files on the way down..." he muttered to himself. Aloud, he asked cheerfully. "Let's go to the shuttle then, shall we?" With that, he leaved the room, his servo-skull flying close behind him.

* * *

2756167.M3.

Mechanicus Small Science Vessel "Proud Spirit"

Close proximity of Relay 314

One of the Sixteen Universal Laws warns: The alien mechanism is a perversion of the True Path. And yet, Magos Xanthis didn't seem to care.

"Yes, yes. Fascinating, isn't?" his mechanical voice was brim with admiration. He was clearly enjoying himself. And did not care about technoheresy he was committing.

Engineer Aubrey Bessemer did not share his enthusiasm.

"Maybe. But is it worth pursuing?" he asked, quietly, so that the crew could not hear him. They were fiercely loyal to Xanthis, for many reasons, one of which was the fact that he had exclusive control over armed servitors onboard.

He also wasn't quite sane. This was also a valid argument to not speak against his wishes.

"Pah! Of course it is. Even if those fools on Mars think otherwise, I can see a vast potential in those devices."

Unfortunately for him, Aubrey knew the circumstances behind the Fabricator-Generals decision to ban any research of strange artifacts that existed in various places of the universe, seemingly at random.

The Emperor came to Mars personally, and very kindly asked him to do it. Rumors said that the ruling body of the Mechanicus was trembling in fear even few weeks later. The Emperor was a kind man, but he was not to be disobeyed.

And this fool wished to do exactly that.

"We will be lucky if they sentence us to Servitude Imperpituis after this." his muttering didn't escape the Xanthis ears. They were augmented, after all.

"Do not worry, Aubrey. After we present them with effects of our research, they will all bow before our greatness. Now, I think we will start of picking apart that end of it. Maybe we will find something that will be useful for our later research." he added, still not getting the gravity of the situation.

Aubrey Bessemer let out a quiet groan of frustration.

It was not going to end well.

Unbeknown to him, a certain xenos was having the exact same thoughts not so far away.

* * *

2157 CE

Turian Recon Frigate "Dagger of Palaven"

Proximity of Relay 314

He looked at the scan results. Yes, it was definitely not going to end well.

"It is confirmed, then?" Captain Toren Vakarian felt the need to ask that question again. Potential war was not something to treat lightly.

"Aye. It would appear that an unknown vessel is currently interfering with the Relay. It looks like... they are trying to take it apart." So even his second in command find it hard to believe his own words. It was a relief.

"And this unknown vessel approximately is of length of..." he asked again, if only to try and elevate his own disbelieve.

"One kilometer, sir. It does not seem to be based on Mass Effect technology. And, luckily for us, it does not seem to be heavily armed either." he added with a smile.

"Thank the spirits for small mercies, hmm?" Probably only ship of the race that was relatively new to space travel. But the potential... it was there. A race that manage to build such ship without the use of Mass Effect Fields. He was impressed.

"What will you have us do, Captain?" The question snapped him out his pondering. The decision had to be made.

Not by him, though.

"It's not our decision to make, Talidros. We take those news to the Primarch. Let him make the call."

"And your predictions, Captain?" he could tell that Talidros was curious. Torens ability to predict higher ups decisions was almost legendary. He smiled.

"By the end of the month, there will be a new client species in our empire."

* * *

Time: Unknown

Location: Unknown

In the dark room, on the equally dark planet, a singular person, clad in shadows, smiled, while banging his fingers against flat top of the ancient looking desk.

"Finally, the game has begun. You have moved your pawns skillfully, as always. But beware. The main players have yet to enter the field." he laughed, quietly "And some of them are unpredictable even to me. What will you do, I wonder. How will you counter them?"

His smile grew, now looking positively vicious.

"And I have already made my opening move."

* * *

Author notes: Well, that took longer than I expected. I'm very sorry for that. Not only life has been not kind on me lately, I have rewriten many things I have planned for this story. It has expended from my initial plans of three books to five, well, technicaly six, because the original books two and three has been merge together in the singular form of book three. Now, with that out of the way, I shall probably pick up the pace.

I also wanted to thank my many reviewers. It's been great, having that much interest in what essentially was the very quick prologue. I also wanted to respond to some concerns raised over said prologue. From this chapter on, I will answer to reviews by sending PMs, but, I'm to took this one exception.

First, the date. Yes, the third millenium is deliberate change. However, it's not the change of setting. It's a change of date. It's pre-heresy, Great Crusade Imperium, only the date is different. As to why... I'm not telling it. Do not worry though. There is a reason for it.

Second, the Ecclesiarchy is not tied to the Inquisition in any way. Well, with the exception of Ordo Hereticus. In fact, the Inquisition pre-dates the Ecclesiarchy. So the Grey Knigts, for that matter. As for the successor chapters, I haven't decided yet. Definitely are not going to be present in the beginning of the story, though.

Third, yes the ME races are going to be buffed. And no, I'm not going to nerf the Imperium down.

Fourth, yes, I know that there were twenty of Primarchs and Legions. Again, it's going to be explained. Also, I'm suprised that not so many people got that.

As for the next chapter, it's going to be longer then the current one. You shall get to know more of the Jack Harpers story, meet two old friends, and some new OC's, as well as see my first attempt at writing space battle.

And last but not least, I wanted to thank the people who help me with the chapter as betas: Sonicanpersonallytellyou, Tamedwolf95, Ursakar, and of course, my brother.


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